Mercurial > repos > dfornika > snippy

comparison snippy_core_wrapper.py @ 17:412683e7a8fe draft

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planemo upload for repository https://github.com/tseemann/snippy commit f4fe84a2dc64bcc8a68de2cdc68c32872294708b-dirty
author dfornika
date Tue, 22 Jan 2019 14:40:08 -0500
parents a69f73853101
children 9d8519bf7a40
comparison
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16:a69f73853101 17:412683e7a8fe
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 2
3 #-------------------------------------- 3 # --------------------------------------
4 # 4 #
5 # snippy_core_wrapper.py 5 # snippy_core_wrapper.py
6 # 6 #
7 # This is an intermediary script between snippy-core.xml and snippy-core 7 # This is an intermediary script between snippy-core.xml and snippy-core
8 # It: 8 # It:
9 # - Copys the supplied zipped snippy output files to the working dir 9 # - Copys the supplied zipped snippy output files to the working dir
10 # - Untars them to their datafile name 10 # - Untars them to their datafile name
11 # - Builds the snippy-core command 11 # - Builds the snippy-core command
12 # - Runs the snippy-core command 12 # - Runs the snippy-core command
13 # 13 #
14 #-------------------------------------- 14 # --------------------------------------
15 15
16 import argparse
16 import os 17 import os
17 import sys
18 import argparse
19 import subprocess 18 import subprocess
20 from shutil import copyfile 19 from shutil import copyfile
21 20
22 def main(): 21 def main():
22
23
23 parser = argparse.ArgumentParser() 24 parser = argparse.ArgumentParser()
24 parser.add_argument('-r', '--ref', help='Reference fasta', required=True) 25 parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
25 parser.add_argument('-i', '--indirs', help='Comma-separated list of input datasets') 26 parser.add_argument('-i', '--indirs', help='Comma-separated list of input datasets')
26 args = parser.parse_args() 27 args = parser.parse_args()
27 28
28 snippy_core_command_line = ['snippy-core', '--ref', args.ref] 29 snippy_core_command_line = ['snippy-core', '--ref', args.ref]
29 30
30 for input_dataset in args.indirs.split(','): 31 for input_dataset in args.indirs.split(','):
31 base_name = os.path.basename(input_dataset) 32 base_name = os.path.basename(input_dataset)
32 print("base_name: " + base_name)
33 copyfile(input_dataset, base_name) 33 copyfile(input_dataset, base_name)
34 subprocess.Popen(['tar', '-xf', base_name]) 34 subprocess.Popen(['tar', '-xf', base_name]).wait()
35 35
36 extracted_dirs = [f for f in os.listdir('.') if os.path.isdir(f) ] 36 extracted_dirs = [f for f in os.listdir('.') if os.path.isdir(f) ]
37 print("extracted_dirs: " + str(extracted_dirs))
38 for extracted_dir in extracted_dirs: 37 for extracted_dir in extracted_dirs:
39 snippy_core_command_line.append(extracted_dir) 38 snippy_core_command_line.append(extracted_dir)
40 print(str(snippy_core_command_line)) 39
41 subprocess.Popen(snippy_core_command_line).wait() 40 subprocess.Popen(snippy_core_command_line).wait()
41
42 42
43 if __name__ == '__main__': 43 if __name__ == '__main__':
44 main() 44 main()